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3D/4D Ophthalmology Image Anaylsis Framework: Continuation of initial January 2017 project by Sungmin Hong:
- Read 4D hyperspectral data
- Viewer and interactor for 3D hi-res image data and 4D hyperspectral data
- Co-registration between 3D hi-res data and 4D hyperspectral data
- Cell segmentation in 3D hi-res data
- Statistics of cells (possibly location, size, distribution)
- Plot of spectra of selected cells or a region-of-interest
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- Review existing modules in 3D Slicer
- Review existing modules for 4D data viewer, such as, multi-volume viewer extension
- Try existing segmentation modules in Slicer to see if they can work on SIM data
- Review existing modules for cell statistics after segmentation
- Implementation/Integration
- Implement/integrate 4D hyperspectral data viewer to show image and spectral information.
- Integrate registration functionality for co-registration between 3D hi-res data and 4D hyperspectral data at image level
- Integrate user-initialized level set segmentation for cell segmentation or EM segmentation module
- Implement a viewer and an interactor for cell statistics
- User Manual
- Create an user manual to comprehend a overview of an extension
- Guide users to different extensions in a algorithmic flow chart if there are any desired functions (registration, segmentation, or etc.) which are already implemented in existing modules.
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- Hyperspectral Analysis
- Implemented a module to convert 4D LSM data to a series of 3D data compatible to MultiVolume Explorer
- With a converted series of 3D data, MultiVolume explorer offered a basic analysis tool for hyperspectral data.
- Label statistics or segmentation need to be added in the future
- Registration
- Basic registration algorithms in Slicer worked well on linear registration between 3D SIM and a cropped and dimension reduced 4D LSM data.
- Detecting corresponding regions of 3D SIM in 4D LSM data needs to be developed in the future.
- Segmentation
- Watershed segmentation on 3D hi-res image data (WASP) was not successful.
- Editor/Segmentation Editor worked good on slice-by-slice segmentation
- Will investigate more on 3D segmentation capability of Slicer with possible collaboration with other groups.
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